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Gothwal SK, Refaat AM, Nakata M, Stanlie A, Honjo T, Begum N. BRD2 promotes antibody class switch recombination by facilitating DNA repair in collaboration with NIPBL. Nucleic Acids Res 2024; 52:4422-4439. [PMID: 38567724 PMCID: PMC11077081 DOI: 10.1093/nar/gkae204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 05/09/2024] Open
Abstract
Efficient repair of DNA double-strand breaks in the Ig heavy chain gene locus is crucial for B-cell antibody class switch recombination (CSR). The regulatory dynamics of the repair pathway direct CSR preferentially through nonhomologous end joining (NHEJ) over alternative end joining (AEJ). Here, we demonstrate that the histone acetyl reader BRD2 suppresses AEJ and aberrant recombination as well as random genomic sequence capture at the CSR junctions. BRD2 deficiency impairs switch (S) region synapse, optimal DNA damage response (DDR), and increases DNA break end resection. Unlike BRD4, a similar bromodomain protein involved in NHEJ and CSR, BRD2 loss does not elevate RPA phosphorylation and R-loop formation in the S region. As BRD2 stabilizes the cohesion loader protein NIPBL in the S regions, the loss of BRD2 or NIPBL shows comparable deregulation of S-S synapsis, DDR, and DNA repair pathway choice during CSR. This finding extends beyond CSR, as NIPBL and BRD4 have been linked to Cornelia de Lange syndrome, a developmental disorder exhibiting defective NHEJ and Ig isotype switching. The interplay between these proteins sheds light on the intricate mechanisms governing DNA repair and immune system functionality.
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Affiliation(s)
- Santosh K Gothwal
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Ahmed M Refaat
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Andre Stanlie
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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2
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Refaat AM, Nakata M, Husain A, Kosako H, Honjo T, Begum NA. HNRNPU facilitates antibody class-switch recombination through C-NHEJ promotion and R-loop suppression. Cell Rep 2023; 42:112284. [PMID: 36943867 DOI: 10.1016/j.celrep.2023.112284] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/23/2022] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
B cells generate functionally different classes of antibodies through class-switch recombination (CSR), which requires classical non-homologous end joining (C-NHEJ) to join the DNA breaks at the donor and acceptor switch (S) regions. We show that the RNA-binding protein HNRNPU promotes C-NHEJ-mediated S-S joining through the 53BP1-shieldin DNA-repair complex. Notably, HNRNPU binds to the S region RNA/DNA G-quadruplexes, contributing to regulating R-loop and single-stranded DNA (ssDNA) accumulation. HNRNPU is an intrinsically disordered protein that interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Strikingly, recruitment of HNRNPU and the C-NHEJ factors is highly sensitive to liquid-liquid phase separation inhibitors, suggestive of DNA-repair condensate formation. We propose that HNRNPU facilitates CSR by forming and stabilizing the C-NHEJ ribonucleoprotein complex and preventing excessive R-loop accumulation, which otherwise would cause persistent DNA breaks and aberrant DNA repair, leading to genomic instability.
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Affiliation(s)
- Ahmed M Refaat
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Hidetaka Kosako
- Division of Cell Signaling, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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3
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Tang C, Krantsevich A, MacCarthy T. Deep learning model of somatic hypermutation reveals importance of sequence context beyond hotspot targeting. iScience 2022; 25:103668. [PMID: 35036866 PMCID: PMC8749460 DOI: 10.1016/j.isci.2021.103668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
B cells undergo somatic hypermutation (SHM) of the Immunoglobulin (Ig) variable region to generate high-affinity antibodies. SHM relies on the activity of activation-induced deaminase (AID), which mutates C>U preferentially targeting WRC (W=A/T, R=A/G) hotspots. Downstream mutations at WA Polymerase η hotspots contribute further mutations. Computational models of SHM can describe the probability of mutations essential for vaccine responses. Previous studies using short subsequences (k-mers) failed to explain divergent mutability for the same k-mer. We developed the DeepSHM (Deep learning on SHM) model using k-mers of size 5-21, improving accuracy over previous models. Interpretation of DeepSHM identified an extended WWRCT motif with particularly high mutability. Increased mutability was further associated with lower surrounding G content. Our model also discovered a conserved AGYCTGGGGG (Y=C/T) motif within FW1 of IGHV3 family genes with unusually high T>G substitution rates. Thus, a wider sequence context increases predictive power and identifies features that drive mutational targeting.
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Affiliation(s)
- Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Artem Krantsevich
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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4
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Zhao H, Hartono SR, de Vera KMF, Yu Z, Satchi K, Zhao T, Sciammas R, Sanz L, Chédin F, Barlow J. Senataxin and RNase H2 act redundantly to suppress genome instability during class switch recombination. eLife 2022; 11:78917. [PMID: 36542058 PMCID: PMC9771370 DOI: 10.7554/elife.78917] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Class switch recombination generates distinct antibody isotypes critical to a robust adaptive immune system, and defects are associated with autoimmune disorders and lymphomagenesis. Transcription is required during class switch recombination to recruit the cytidine deaminase AID-an essential step for the formation of DNA double-strand breaks-and strongly induces the formation of R loops within the immunoglobulin heavy-chain locus. However, the impact of R loops on double-strand break formation and repair during class switch recombination remains unclear. Here, we report that cells lacking two enzymes involved in R loop removal-senataxin and RNase H2-exhibit increased R loop formation and genome instability at the immunoglobulin heavy-chain locus without impacting its transcriptional activity, AID recruitment, or class switch recombination efficiency. Senataxin and RNase H2-deficient cells also exhibit increased insertion mutations at switch junctions, a hallmark of alternative end joining. Importantly, these phenotypes were not observed in cells lacking senataxin or RNase H2B alone. We propose that senataxin acts redundantly with RNase H2 to mediate timely R loop removal, promoting efficient repair while suppressing AID-dependent genome instability and insertional mutagenesis.
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Affiliation(s)
- Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | | | - Zheyuan Yu
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States,Graduate Group in Biostatistics, University of California, DavisDavisUnited States
| | - Krishni Satchi
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Tracy Zhao
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California, DavisDavisUnited States
| | - Lionel Sanz
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Jacqueline Barlow
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
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5
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Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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6
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Kuznetsov VA, Bondarenko V, Wongsurawat T, Yenamandra SP, Jenjaroenpun P. Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers. Nucleic Acids Res 2019; 46:7566-7585. [PMID: 29945198 PMCID: PMC6125637 DOI: 10.1093/nar/gky554] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/08/2018] [Indexed: 12/31/2022] Open
Abstract
R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we generated a quantitative R-loop forming sequence (RLFS) model, quantitative model of R-loop-forming sequences (QmRLFS) and predicted ∼660 000 RLFSs; most of them located in genes and gene-flanking regions, G-rich regions and disease-associated genomic loci in the human genome. Here, we conducted a comprehensive comparative analysis of these RLFSs using experimental data and demonstrated the high performance of QmRLFS predictions on the nucleotide and genome scales. The preferential co-localization of RLFS with promoters, U1 splice sites, gene ends, enhancers and non-B DNA structures, such as G-quadruplexes, provides evidence for the mechanical linkage between DNA tertiary structures, transcription initiation and R-loops in critical regulatory genome regions. We introduced and characterized an abundant class of reverse-forward RLFS clusters highly enriched in non-B DNA structures, which localized to promoters, gene ends and enhancers. The RLFS co-localization with promoters and transcriptionally active enhancers suggested new models for in cis and in trans regulation by RNA:DNA hybrids of transcription initiation and formation of 3D-chromatin loops. Overall, this study provides a rationale for the discovery and characterization of the non-B DNA regulatory structures involved in the formation of the RNA:DNA interactome as the basis for an emerging quantitative R-loop biology and pathobiology.
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Affiliation(s)
- Vladimir A Kuznetsov
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Vladyslav Bondarenko
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Thidathip Wongsurawat
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Surya P Yenamandra
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Piroon Jenjaroenpun
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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7
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Dalloul I, Boyer F, Dalloul Z, Pignarre A, Caron G, Fest T, Chatonnet F, Delaloy C, Durandy A, Jeannet R, Lereclus E, Boutouil H, Aldigier JC, Péron S, Le Noir S, Cook-Moreau J, Cogné M. Locus suicide recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues. PLoS Genet 2019; 15:e1007721. [PMID: 31199803 PMCID: PMC6594652 DOI: 10.1371/journal.pgen.1007721] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 06/26/2019] [Accepted: 05/14/2019] [Indexed: 12/24/2022] Open
Abstract
B-cell activation yields abundant cell death in parallel to clonal amplification and remodeling of immunoglobulin (Ig) genes by activation-induced deaminase (AID). AID promotes affinity maturation of Ig variable regions and class switch recombination (CSR) in mature B lymphocytes. In the IgH locus, these processes are under control of the 3' regulatory region (3'RR) super-enhancer, a region demonstrated in the mouse to be both transcribed and itself targeted by AID-mediated recombination. Alternatively to CSR, IgH deletions joining Sμ to "like-switch" DNA repeats that flank the 3' super-enhancer can thus accomplish so-called "locus suicide recombination" (LSR) in mouse B-cells. Using an optimized LSR-seq high throughput method, we now show that AID-mediated LSR is evolutionarily conserved and also actively occurs in humans, providing an activation-induced cell death pathway in multiple conditions of B-cell activation. LSR either focuses on the functional IgH allele or is bi-allelic, and its signature is mainly detected when LSR is ongoing while it vanishes from fully differentiated plasma cells or from "resting" blood memory B-cells. Highly diversified breakpoints are distributed either within the upstream (3'RR1) or downstream (3'RR2) copies of the IgH 3' super-enhancer and all conditions activating CSR in vitro also seem to trigger LSR although TLR ligation appeared the most efficient. Molecular analysis of breakpoints and junctions confirms that LSR is AID-dependent and reveals junctional sequences somehow similar to CSR junctions but with increased usage of microhomologies.
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Affiliation(s)
- Iman Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - François Boyer
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Zeinab Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Gersende Caron
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | - Thierry Fest
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Céline Delaloy
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Robin Jeannet
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Emilie Lereclus
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Hend Boutouil
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Sophie Péron
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Sandrine Le Noir
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
| | - Michel Cogné
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
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8
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Belotserkovskii BP, Tornaletti S, D'Souza AD, Hanawalt PC. R-loop generation during transcription: Formation, processing and cellular outcomes. DNA Repair (Amst) 2018; 71:69-81. [PMID: 30190235 PMCID: PMC6340742 DOI: 10.1016/j.dnarep.2018.08.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.
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Affiliation(s)
- Boris P Belotserkovskii
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Silvia Tornaletti
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Alicia D D'Souza
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Philip C Hanawalt
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States.
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9
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Huang T, Wang X, Si R, Chi H, Han B, Han H, Cao G, Zhao Y. Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon ( Columba livia) IgH Gene Locus. THE JOURNAL OF IMMUNOLOGY 2018; 200:3720-3728. [PMID: 29686053 DOI: 10.4049/jimmunol.1701768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/27/2018] [Indexed: 11/19/2022]
Abstract
Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon (Columba livia) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds.
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Affiliation(s)
- Tian Huang
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, People's Republic of China
| | - Xifeng Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100193, People's Republic of China; and
| | - Run Si
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, People's Republic of China
| | - Hao Chi
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, People's Republic of China
| | - Binyue Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Gengsheng Cao
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, People's Republic of China;
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
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10
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Yewdell WT, Chaudhuri J. A transcriptional serenAID: the role of noncoding RNAs in class switch recombination. Int Immunol 2018; 29:183-196. [PMID: 28535205 DOI: 10.1093/intimm/dxx027] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/22/2017] [Indexed: 12/31/2022] Open
Abstract
During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions and requires the DNA-modifying enzyme activation-induced cytidine deaminase (AID). AID-mediated DNA deamination within S regions initiates the formation of DNA double-strand breaks, which serve as biochemical beacons for downstream DNA repair pathways that coordinate the ligation of DNA breaks. Myriad factors contribute to optimal AID targeting; however, many of these factors also localize to genomic regions outside of the Igh locus. Thus, a current challenge is to explain the specific targeting of AID to the Igh locus. Recent studies have implicated noncoding RNAs in CSR, suggesting a provocative mechanism that incorporates Igh-specific factors to enable precise AID targeting. Here, we chronologically recount the rich history of noncoding RNAs functioning in CSR to provide a comprehensive context for recent and future discoveries. We present a model for the RNA-guided targeting of AID that attempts to integrate historical and recent findings, and highlight potential caveats. Lastly, we discuss testable hypotheses ripe for current experimentation, and explore promising ideas for future investigations.
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Affiliation(s)
- William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer, New York, NY 10065, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
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11
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Moriyama K, Yoshizawa-Sugata N, Masai H. Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture. J Biol Chem 2018; 293:3607-3624. [PMID: 29348174 DOI: 10.1074/jbc.ra117.000446] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/21/2017] [Indexed: 11/06/2022] Open
Abstract
Rap1-interacting protein 1 (Rif1) regulates telomere length in budding yeast. We previously reported that, in metazoans and fission yeast, Rif1 also plays pivotal roles in controlling genome-wide DNA replication timing. We proposed that Rif1 may assemble chromatin compartments that contain specific replication-timing domains by promoting chromatin loop formation. Rif1 also is involved in DNA lesion repair, restart after replication fork collapse, anti-apoptosis activities, replicative senescence, and transcriptional regulation. Although multiple physiological functions of Rif1 have been characterized, biochemical and structural information on mammalian Rif1 is limited, mainly because of difficulties in purifying the full-length protein. Here, we expressed and purified the 2418-amino-acid-long, full-length murine Rif1 as well as its partially truncated variants in human 293T cells. Hydrodynamic analyses indicated that Rif1 forms elongated or extended homo-oligomers in solution, consistent with the presence of a HEAT-type helical repeat segment known to adopt an elongated shape. We also observed that the purified murine Rif1 bound G-quadruplex (G4) DNA with high specificity and affinity, as was previously shown for Rif1 from fission yeast. Both the N-terminal (HEAT-repeat) and C-terminal segments were involved in oligomer formation and specifically bound G4 DNA, and the central intrinsically disordered polypeptide segment increased the affinity for G4. Of note, pulldown assays revealed that Rif1 simultaneously binds multiple G4 molecules. Our findings support a model in which Rif1 modulates chromatin loop structures through binding to multiple G4 assemblies and by holding chromatin fibers together.
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Affiliation(s)
- Kenji Moriyama
- From the Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Naoko Yoshizawa-Sugata
- From the Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hisao Masai
- From the Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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12
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Chen L, Chen JY, Zhang X, Gu Y, Xiao R, Shao C, Tang P, Qian H, Luo D, Li H, Zhou Y, Zhang DE, Fu XD. R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Mol Cell 2017; 68:745-757.e5. [PMID: 29104020 PMCID: PMC5957070 DOI: 10.1016/j.molcel.2017.10.008] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/05/2017] [Accepted: 10/06/2017] [Indexed: 12/18/2022]
Abstract
R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed.
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Affiliation(s)
- Liang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Xuan Zhang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Ying Gu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Rui Xiao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Peng Tang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Hao Qian
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Daji Luo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yu Zhou
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Dong-Er Zhang
- Department of Pathology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.
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13
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RNA Polymerase Collision versus DNA Structural Distortion: Twists and Turns Can Cause Break Failure. Mol Cell 2017; 62:327-334. [PMID: 27153532 DOI: 10.1016/j.molcel.2016.03.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The twisting of DNA due to the movement of RNA polymerases is the basis of numerous classic experiments in molecular biology. Recent mouse genetic models indicate that chromosomal breakage is common at sites of transcriptional turbulence. Two key studies on this point mapped breakpoints to sites of either convergent or divergent transcription but arrived at different conclusions as to which is more detrimental and why. The issue hinges on whether DNA strand separation is the basis for the chromosomal instability or collision of RNA polymerases.
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Pavri R. R Loops in the Regulation of Antibody Gene Diversification. Genes (Basel) 2017; 8:E154. [PMID: 28574479 PMCID: PMC5485518 DOI: 10.3390/genes8060154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/24/2017] [Accepted: 05/31/2017] [Indexed: 01/06/2023] Open
Abstract
For nearly three decades, R loops have been closely linked with class switch recombination (CSR), the process that generates antibody isotypes and that occurs via a complex cascade initiated by transcription-coupled mutagenesis in switch recombination sequences. R loops form during transcription of switch recombination sequences in vitro and in vivo, and there is solid evidence that R loops are required for efficient class switching. The classical model of R loops posits that they boost mutation rates by generating stable and long tracts of single-stranded DNA that serve as the substrate for activation induced deaminase (AID), the enzyme that initiates the CSR reaction cascade by co-transcriptionally mutating ssDNA in switch recombination sequences. Though logical and compelling, this model has not been supported by in vivo evidence. Indeed, several reports suggest that R loops may not be involved in recruiting AID activity to switch regions, meaning that R loops probably serve other unanticipated roles in CSR. Here, I review the key findings in this field to date and propose hypotheses that could help towards elucidating the precise function of R loops in CSR.
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Affiliation(s)
- Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus Vienna Biocenter-1, Vienna Biocenter, Vienna 1030, Austria.
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15
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Halász L, Karányi Z, Boros-Oláh B, Kuik-Rózsa T, Sipos É, Nagy É, Mosolygó-L Á, Mázló A, Rajnavölgyi É, Halmos G, Székvölgyi L. RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases. Genome Res 2017; 27:1063-1073. [PMID: 28341774 PMCID: PMC5453320 DOI: 10.1101/gr.219394.116] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/23/2017] [Indexed: 12/16/2022]
Abstract
The impact of R-loops on the physiology and pathology of chromosomes has been demonstrated extensively by chromatin biology research. The progress in this field has been driven by technological advancement of R-loop mapping methods that largely relied on a single approach, DNA-RNA immunoprecipitation (DRIP). Most of the DRIP protocols use the experimental design that was developed by a few laboratories, without paying attention to the potential caveats that might affect the outcome of RNA-DNA hybrid mapping. To assess the accuracy and utility of this technology, we pursued an analytical approach to estimate inherent biases and errors in the DRIP protocol. By performing DRIP-sequencing, qPCR, and receiver operator characteristic (ROC) analysis, we tested the effect of formaldehyde fixation, cell lysis temperature, mode of genome fragmentation, and removal of free RNA on the efficacy of RNA-DNA hybrid detection and implemented workflows that were able to distinguish complex and weak DRIP signals in a noisy background with high confidence. We also show that some of the workflows perform poorly and generate random answers. Furthermore, we found that the most commonly used genome fragmentation method (restriction enzyme digestion) led to the overrepresentation of lengthy DRIP fragments over coding ORFs, and this bias was enhanced at the first exons. Biased genome sampling severely compromised mapping resolution and prevented the assignment of precise biological function to a significant fraction of R-loops. The revised workflow presented herein is established and optimized using objective ROC analyses and provides reproducible and highly specific RNA-DNA hybrid detection.
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Affiliation(s)
- László Halász
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Internal Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Beáta Boros-Oláh
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Tímea Kuik-Rózsa
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Sipos
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Biopharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Nagy
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Ágnes Mosolygó-L
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Anett Mázló
- Department of Immunology, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Rajnavölgyi
- Department of Immunology, University of Debrecen, 4032 Debrecen, Hungary
| | - Gábor Halmos
- Department of Biopharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
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16
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Jenjaroenpun P, Wongsurawat T, Sutheeworapong S, Kuznetsov VA. R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. Nucleic Acids Res 2017; 45:D119-D127. [PMID: 27899586 PMCID: PMC5210542 DOI: 10.1093/nar/gkw1054] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 10/04/2016] [Accepted: 10/20/2016] [Indexed: 11/18/2022] Open
Abstract
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1 565 795 RLFSs distributed in 121 056 genic or proximal gene regions of the covered organisms. It provides a comprehensive annotation of Ensembl RLFS-positive genes including 93 454 protein coding genes, 12 480 long non-coding RNA and 7 568 small non-coding RNA genes and 7 554 pseudogenes. Using new interface and genome viewers of R-loopDB, users can search the gene(s) in multiple species with keywords in a single query. R-loopDB provides tools to carry out comparative evolution and genome-scale analyses in R-loop biology.
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Affiliation(s)
- Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, 138671, Singapore
| | - Thidathip Wongsurawat
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, 138671, Singapore
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Research, Pilot Plant Development and Training Institute, King Mongkut's University of Technology, Thonburi, Bangkok, Thailand
| | - Vladimir A Kuznetsov
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, 138671, Singapore
- School of Computer Engineering, Nanyang Technological University, 639798, Singapore
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17
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Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures. DNA Repair (Amst) 2016; 45:1-24. [DOI: 10.1016/j.dnarep.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
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18
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Abstract
Analysis of chromosomal translocation sequence locations in human lymphomas has provided valuable clues about the mechanism of the translocations and when they occur. Biochemical analyses on the mechanisms of DNA breakage and rejoining permit formulation of detailed models of the human chromosomal translocation process in lymphoid neoplasms. Most human lymphomas are derived from B cells in which a DNA break at an oncogene is initiated by activation-induced deaminase (AID). The partner locus in many cases is located at one of the antigen receptor loci, and this break is generated by the recombination activating gene (RAG) complex or by AID. After breakage, the joining process typically occurs by non-homologous DNA end-joining (NHEJ). Some of the insights into this mechanism also apply to translocations that occur in non-lymphoid neoplasms.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Center, Room 5428, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, MC9176, Los Angeles, California 90089-9176, USA
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19
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Zhang ZZ, Pannunzio NR, Lu Z, Hsu E, Yu K, Lieber MR. The repetitive portion of the Xenopus IgH Mu switch region mediates orientation-dependent class switch recombination. Mol Immunol 2015; 67:524-31. [PMID: 26277278 DOI: 10.1016/j.molimm.2015.07.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/26/2022]
Abstract
Vertebrates developed immunoglobulin heavy chain (IgH) class switch recombination (CSR) to express different IgH constant regions. Most double-strand breaks for Ig CSR occur within the repetitive portion of the switch regions located upstream of each set of constant domain exons for the Igγ, Igα or Igϵ heavy chain. Unlike mammalian switch regions, Xenopus switch regions do not have a high G-density on the non-template DNA strand. In previous studies, when Xenopus Sμ DNA was moved to the genome of mice, it is able to support substantial CSR when it is used to replace the murine Sγ1 region. Here, we tested both the 2kb repetitive portion and the 4.6 kb full-length portions of the Xenopus Sμ in both their natural (forward) orientation relative to the constant domain exons, as well as the opposite (reverse) orientation. Consistent with previous work, we find that the 4.6 kb full-length Sμ mediates similar levels of CSR in both the forward and reverse orientations. Whereas, the forward orientation of the 2kb portion can restore the majority of the CSR level of the 4.6 kb full-length Sμ, the reverse orientation poorly supports R-looping and no CSR. The forward orientation of the 2kb repetitive portion has more GG dinucleotides on the non-template strand than the reverse orientation. The correlation of R-loop formation with CSR efficiency, as demonstrated in the 2kb repetitive fragment of the Xenopus switch region, confirms a role played by R-looping in CSR that appears to be conserved through evolution.
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Affiliation(s)
- Zheng Z Zhang
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
| | - Nicholas R Pannunzio
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
| | - Zhengfei Lu
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, New York, NY 11203, United States
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI 48824, United States
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
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20
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Blombery PA, Wall M, Seymour JF. The molecular pathogenesis of B-cell non-Hodgkin lymphoma. Eur J Haematol 2015; 95:280-93. [DOI: 10.1111/ejh.12589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 12/17/2022]
Affiliation(s)
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service; St Vincent's Hospital Melbourne; University of Melbourne; Fitzroy Vic. Australia
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21
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Zhang ZZ, Hsieh CL, Okitsu CY, Han L, Yu K, Lieber MR. Effect of CpG dinucleotides within IgH switch region repeats on immunoglobulin class switch recombination. Mol Immunol 2015; 66:284-9. [PMID: 25899867 DOI: 10.1016/j.molimm.2015.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/31/2015] [Accepted: 04/04/2015] [Indexed: 12/30/2022]
Abstract
Immunoglobulin (Ig) heavy chains undergo class switch recombination (CSR) to change the heavy chain isotype from IgM to IgG, A or E. The switch regions are several kilobases long, repetitive, and G-rich on the nontemplate strand. They are also relatively depleted of CpG (also called CG) sites for unknown reasons. Here we use synthetic switch regions at the IgH switch alpha (Sα) locus to test the effect of CpG sites and to try to understand why the IgH switch sequences evolved to be relatively depleted of CpG. We find that even just two CpG sites within an 80 bp synthetic switch repeat iterated 15 times (total switch region length of 1200 bp containing 30 CpG sites) are sufficient to dramatically reduce both Ig CSR and transcription through the switch region from the upstream Iα sterile transcript promoter, which is the promoter that directs transcripts through the Sα region. De novo DNA methylation occurs at the four CpG sites in and around the Iα promoter when each 80 bp Iα switch repeat contains the two CpG sites. Thus, a relatively low density of CpG sites within the switch repeats can induce upstream CpG methylation at the IgH alpha locus, and cause a substantial decrease in transcription from the sterile transcript promoter. This effect is likely the reason that switch regions evolved to contain very few CpG sites. We discuss these findings as they relate to DNA methylation and to Ig CSR.
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Affiliation(s)
- Zheng Z Zhang
- USC Norris Comprehensive Cancer Center, Molecular and Computational Biology Program, Department of Biological Sciences; Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA 90089-9176, United States
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Center, Molecular and Computational Biology Program, Department of Biological Sciences; Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA 90089-9176, United States
| | - Cindy Yen Okitsu
- USC Norris Comprehensive Cancer Center, Molecular and Computational Biology Program, Department of Biological Sciences; Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA 90089-9176, United States
| | - Li Han
- Department of Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI 48824, United States
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI 48824, United States.
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, Molecular and Computational Biology Program, Department of Biological Sciences; Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA 90089-9176, United States.
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22
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Jenjaroenpun P, Wongsurawat T, Yenamandra SP, Kuznetsov VA. QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences. Nucleic Acids Res 2015; 43:W527-34. [PMID: 25883153 PMCID: PMC4489302 DOI: 10.1093/nar/gkv344] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/06/2015] [Indexed: 11/17/2022] Open
Abstract
The possible formation of three-stranded RNA and DNA hybrid structures (R-loops) in thousands of functionally important guanine-rich genic and inter-genic regions could suggest their involvement in transcriptional regulation and even development of diseases. Here, we introduce the first freely available R-loop prediction program called Quantitative Model of R-loop Forming Sequence (RLFS) finder (QmRLFS-finder), which predicts RLFSs in nucleic acid sequences based on experimentally supported structural models of RLFSs. QmRLFS-finder operates via a web server or a stand-alone command line tool. This tool identifies and visualizes RLFS coordinates from any natural or artificial DNA or RNA input sequences and creates standards-compliant output files for further annotation and analysis. QmRLFS-finder demonstrates highly accurate predictions of the detected RLFSs, proposing new perspective to further discoveries in R-loop biology, biotechnology and molecular therapy. QmRLFS-finder is freely available at http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder.
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Affiliation(s)
- Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671
| | - Thidathip Wongsurawat
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671
| | - Surya Pavan Yenamandra
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671
| | - Vladimir A Kuznetsov
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671
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23
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Zhang ZZ, Pannunzio NR, Hsieh CL, Yu K, Lieber MR. Complexities due to single-stranded RNA during antibody detection of genomic rna:dna hybrids. BMC Res Notes 2015; 8:127. [PMID: 25890199 PMCID: PMC4393563 DOI: 10.1186/s13104-015-1092-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/24/2015] [Indexed: 12/21/2022] Open
Abstract
Background Long genomic R-loops in eukaryotes were first described at the immunoglobulin heavy chain locus switch regions using bisulfite sequencing and functional studies. A mouse monoclonal antibody called S9.6 has been used for immunoprecipitation (IP) to identify R-loops, based on the assumption that it is specific for RNA:DNA over other nucleic acid duplexes. However, recent work has demonstrated that a variable domain of S9.6 binds AU-rich RNA:RNA duplexes with a KD that is only 5.6-fold weaker than for RNA:DNA duplexes. Most IP protocols do not pre-clear the genomic nucleic acid with RNase A to remove free RNA. Fold back of ssRNA can readily generate RNA:RNA duplexes that may bind the S9.6 antibody, and adventitious binding of RNA may also create short RNA:DNA regions. Here we investigate whether RNase A is needed to obtain reliable IP with S9.6. Findings As our test locus, we chose the most well-documented site for kilobase-long mammalian genomic R-loops, the immunoglobulin heavy chain locus (IgH) class switch regions. The R-loops at this locus can be induced by using cytokines to stimulate transcription from germline transcript promoters. We tested IP using S9.6 with and without various RNase treatments. The RNase treatments included RNase H to destroy the RNA in an RNA:DNA duplex and RNase A to destroy single-stranded (ss) RNA to prevent it from binding S9.6 directly (as duplex RNA) and to prevent the ssRNA from annealing to the genome, resulting in adventitious RNA:DNA hybrids. We find that optimal detection of RNA:DNA duplexes requires removal of ssRNA using RNase A. Without RNase A treatment, known regions of R-loop formation containing RNA:DNA duplexes can not be reliably detected. With RNase A treatment, a signal can be detected over background, but only within a limited 2 or 3-fold range, even with a stable kilobase-long genomic R-loop. Conclusion Any use of the S9.6 antibody must be preceded by RNase A treatment to remove free ssRNA that may compete for the S9.6 binding by forming RNA:RNA regions or short, transient RNA:DNA duplexes. Caution should be used when interpreting S9.6 data, and confirmation by independent structural and functional methods is essential. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1092-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zheng Z Zhang
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA. .,Departments of Pathology, Biochemistry & Molecular Biology; Molecular Microbiology & Immunology; Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA.
| | - Nicholas R Pannunzio
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA. .,Departments of Pathology, Biochemistry & Molecular Biology; Molecular Microbiology & Immunology; Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA.
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA. .,Departments of Pathology, Biochemistry & Molecular Biology; Molecular Microbiology & Immunology; Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA.
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI, 48824, USA.
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA. .,Departments of Pathology, Biochemistry & Molecular Biology; Molecular Microbiology & Immunology; Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, USA.
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